AMBER Archive (2003)

Subject: RE: Velocity

From: Yong Duan (yduan_at_udel.edu)
Date: Mon Feb 17 2003 - 15:00:01 CST

Dear Hungie:

Do you have any particular reason why you need per-step velocities? We
probably can suggest a few alternatives other than re-run the trajectory
if you can let us know a bit more detail of your objectives.

Yong
********
From: "A. Hungie" <hungie01_at_hotmail.com>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Monday, February 17, 2003 11:01 AM
Subject: Velocity

> Dear All,
>
> I have done MD simulations of DNA. In my trajectory file, there were
> only coordinates of all atoms and box size, no velocity. Could anyone
> tell me
how
> I can calculate velocity of any atom? I would like to know, for
> example, velocity of atom N9 of residue 4 at the time 200th ps. I
> don't want to re-run the production to store coordinates and
> velocities. Thank you very much in advance.
>
> Hungie
>